Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MCM2

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
Colon carcinoma
cell line
HCT116
cell type
Cultured cancer cell line
genotype
WT
chip antibody
pS40/41 MCM2 antibody (Bethyl Labs, A300788A)
molecule subtype
ChipSeq DNA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
DNA from cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. For ChipSeq, DNA molecules were enriched using antibodies against proteins of interest. Enriched ChIPed DNA molecules were sequenced by Illumina NextSeq 75 cycle High Output kit with single ennd of 75bp. For nascent DNA, re-replicated DNA, paired-end libraries of genomic DNA (gDNA) were prepared using Illumina TruSeq Nano DNA Library Prep kits. Control genomic DNA was fragmented to ~ 400 bp insert size on the Covaris which generates dsDNA fragments with 3' or 5' overhangs. The sheared DNA was blunt-ended and library size selection was done using sample purification beads. A single 'A' nucleotide was added to the 3' ends of the blunt fragments to prevent them from ligating to each other during the adapter ligation reaction. A corresponding single 'T' nucleotide on the 3' end of the adapter provided a complementary overhang for ligating the adapter to the fragment. The indexed adapters were ligated to the ends of the DNA fragments and then PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product was then quantitated by qPCR before cluster generation and sequencing.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
31005709
Reads aligned (%)
99.5
Duplicates removed (%)
37.3
Number of peaks
4385 (qval < 1E-05)

hg19

Number of total reads
31005709
Reads aligned (%)
99.6
Duplicates removed (%)
37.9
Number of peaks
4321 (qval < 1E-05)

Base call quality data from DBCLS SRA